Tool to find 3' tailing of non-coding RNAs
Project description
Tailer: A tool for 3' end analysis of non-polyadenylated RNAs from 3' sequencing data
Requirements
Python >= 3.6
pysam
Bio
gffuitls
requests
tqdm
Installation
pip install jla-tailer
Usage
Global alignment with a GTF annotation and SAM/BAM formatted files
Tailer -a [GTF Annotation] [SAM or BAM Files]
Local alignment with with FASTA/Q and specific Ensembl IDs of interest
Tailer -e [comma separated list of EnsIDs no spaces] [FASTA/Q files]
Optional arguments
-t, --threshold [int, default=100]
- Any alignment identified further than this distance in nucleotides from the mature end will be considered spurious and discarded
-x, --trim [int, default=0]
- Helper for local mode only, can remove X nucleotides from adapter on the 3' end
-r, --rev_comp
- Helper for local mode only. If set, will reverse complement the reads which is necessary for the Lykke-Andersen pipeline
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
jla-tailer-0.0.15.tar.gz
(9.9 kB
view hashes)
Built Distribution
Close
Hashes for jla_tailer-0.0.15-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 337644b8e1d429baa87cb8b4c2609b954a07ff460b3ef4bc74468f5f829ec03d |
|
MD5 | 5c1fb65da486c1b12c61b821b1b53839 |
|
BLAKE2b-256 | c5c695e2e3ca865008e7656ec27ed07865b386a5c3925bb88a52fd6d66549283 |